There is a clear need to have available anti-malarial drugs with targets different from those affected by agents for which resistance is widespread in the field. Because of the critical role played by mitochondria in eukaryotic organisms, they could form such targets. The challenge is to find compounds that affect the parasite mitochondrial physiology without affecting the host mitochondria. We previously identified several aspects of mitochondrial genetics and biochemistry of malaria parasites that could potentially be affected in a selective manner. Atovaquone, a newly developed broad-spectrum anti-parasite drug, selectively inhibits electron transport in malarial mitochondria, and was shown to collapse electropotential across the inner mitochondrial membrane in the parasites. Atovaquone as a single agent leads to unacceptable level of treatment failure, requiring the inclusion of synergistic drug, proguanil. Our investigations have provided clues as to the mechanism for this synergy, and a potential explanation for the relative lack of resistance emergence. To continue our investigations, we propose experiments that will extend the understanding of anti-mitochondrial drug action and resistance, and derive a more detailed view of mitochondrial physiology in malaria parasites. Mechanisms of drug action and resistance will be investigated by using genetic and biochemical tools that have been developed in our laboratory. The Malaria Genome Project is fast approaching completion of the entire DNA sequence of Plasmodium falciparum, and to use this information for further insights into mitochondrial physiology of the parasites, nuclearly encoded mitochondrial genes will be identified and their expression patterns will be determined. To develop tools for studying mitochondrial physiology in malaria parasites, genetic approaches will be used to identify signal sequences that direct nuclearly encoded proteins to the malarial mitochondria. These tools will be valuable for experimental testing of hypotheses regarding mitochondrial functions in malaria parasites. In summer, an integrated approach is proposed to develop a mechanistic and functional view of mitochondrial physiology of malaria parasites.. The approach of selective targeting parasite mitochondrion by anti-parasitic drugs has been established by the advent of atovaquone. Our proposed studies will derive better mechanistic insights into drug action to help future drug development strategies. The studies proposed will also provide basic information on parasite mitochondrial functions with a hope that these too can form the basis from which other effective means for malaria treatment can be developed.